scholarly journals Data Mining of Coronavirus: SARS-CoV-2, SARS-CoV and MERS-CoV

2021 ◽  
Author(s):  
Jung Eun Huh ◽  
Seunghee Han ◽  
Taeseon Yoon
Keyword(s):  
Data Mining ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Decision Tree ◽  
High Similarity ◽  
Incubation Periods ◽  
Initial Question ◽  
Non Linear ◽  
The Difference

Abstract Objectives: All three SARS-CoV-2, SARS-CoV and MERS-CoV belong to the Coronaviridae family. In this study we compare amino acid and codon sequence of SARS-CoV-2, SARS-CoV and MERS-CoV using different statistics programs to understand their characteristics. Specifically, we are interested in how differences in the amino acid and codon sequence lead to different incubation periods and outbreak periods.Results: The initial question we had was to compare SARS-CoV-2 to different viruses in the coronavirus family to understand its characteristics. The result of experiments using BLAST, Apriori and Decision Tree has shown that SARS-CoV-2 had high similarity with SARS-CoV while having comparably low similarity with MERS-CoV. We decided to compare the codons of SARS-CoV-2 and MERS-CoV to see the difference. Though the viruses are very alike according to BLAST and Apriori experiments, SVM proved that they can be effectively classified using non-linear kernels. Decision Tree experiment has proved several remarkable properties of SARS-CoV-2 amino acid sequence that cannot be found in MERS-CoV amino acid sequence.The consequential purpose of this paper is to minimize the damage on humanity from SARS-CoV-2. Hence, further studies can focus on the comparison of SARS-CoV-2 virus with other viruses that also can be transmitted during latent periods.

scholarly journals Data mining of coronavirus: SARS-CoV-2, SARS-CoV and MERS-CoV

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Jung Eun Huh ◽  
Seunghee Han ◽  
Taeseon Yoon
Keyword(s):  
Machine Learning ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Decision Tree ◽  
Machine Learning Algorithms ◽  
High Similarity ◽  
Incubation Periods ◽  
Initial Question ◽  
The Difference ◽  
Blast Program

Abstract Objective In this study we compare the amino acid and codon sequence of SARS-CoV-2, SARS-CoV and MERS-CoV using different statistics programs to understand their characteristics. Specifically, we are interested in how differences in the amino acid and codon sequence can lead to different incubation periods and outbreak periods. Our initial question was to compare SARS-CoV-2 to different viruses in the coronavirus family using BLAST program of NCBI and machine learning algorithms. Results The result of experiments using BLAST, Apriori and Decision Tree has shown that SARS-CoV-2 had high similarity with SARS-CoV while having comparably low similarity with MERS-CoV. We decided to compare the codons of SARS-CoV-2 and MERS-CoV to see the difference. Though the viruses are very alike according to BLAST and Apriori experiments, SVM proved that they can be effectively classified using non-linear kernels. Decision Tree experiment proved several remarkable properties of SARS-CoV-2 amino acid sequence that cannot be found in MERS-CoV amino acid sequence. The consequential purpose of this paper is to minimize the damage on humanity from SARS-CoV-2. Hence, further studies can be focused on the comparison of SARS-CoV-2 virus with other viruses that also can be transmitted during latent periods.

Sequence mutations in teleost cardiac troponin C that are permissive of high Ca2+ affinity of site II

2003 ◽  
Vol 284 (5) ◽  
pp. C1176-C1184 ◽  
Author(s):  
Todd E. Gillis ◽  
Chris D. Moyes ◽  
Glen F. Tibbits
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Cardiac Troponin ◽  
Troponin C ◽  
Fluorescent Reporter ◽  
Cardiac Troponin C ◽  
The Difference ◽  
Higher Sensitivity

Cardiac myofibrils isolated from trout heart have been demonstrated to have a higher sensitivity for Ca2+ than mammalian cardiac myofibrils. Using cardiac troponin C (cTnC) cloned from trout and mammalian hearts, we have previously demonstrated that this comparatively high Ca2+ sensitivity is due, in part, to trout cTnC (ScTnC) having twice the Ca2+ affinity of mammalian cTnC (McTnC) over a broad range of temperatures. The amino acid sequence of ScTnC is 92% identical to McTnC. To determine the residues responsible for the high Ca2+ affinity, the function of a number of ScTnC and McTnC mutants was characterized by monitoring an intrinsic fluorescent reporter that monitors Ca2+ binding to site II (F27W). The removal of the COOH terminus (amino acids 90–161) from ScTnC and McTnC maintained the difference in Ca2+ affinity between the truncated cTnC isoforms (ScNTnC and McNTnC). The replacement of Gln29 and Asp30 in ScNTnC with the corresponding residues from McNTnC, Leu and Gly, respectively, reduced Ca2+ affinity to that of McNTnC. These results demonstrate that Gln29 and Asp30 in ScTnC are required for the high Ca2+ affinity of site II.

scholarly journals Streptococcus mutans Strains Harboring Collagen-binding Adhesin

2004 ◽  
Vol 83 (7) ◽  
pp. 534-539 ◽  
Author(s):  
Y. Sato ◽  
K. Okamoto ◽  
A. Kagami ◽  
Y. Yamamoto ◽  
T. Igarashi ◽  
...  
Keyword(s):  
Amino Acid ◽  
Recombinant Protein ◽  
Amino Acid Sequence ◽  
Streptococcus Mutans ◽  
Parental Strain ◽  
Random Mutagenesis ◽  
Gene Fragment ◽  
High Similarity ◽  
Collagen Binding ◽  
Negative Mutant

A previously unidentified 120-kDa protein was detected in Streptococcus mutans strain Z1 and was involved in the cold-agglutination of the strain. We have identified the gene, designated cnm, as being involved in the agglutination of strain Z1 following random mutagenesis. The amino acid sequence of the deduced Cnm protein exhibited high similarity to those of collagen-binding adhesins from staphylococci and other organisms. To confirm whether the protein is involved in collagen-binding, we cloned a cnm gene fragment, overexpressed it in E.coli, and prepared crude extracts. The extracts containing recombinant protein exhibited binding to immobilized collagen and laminin but not to fibronectin. Compared with the parental strain Z1, the cold-agglutination-negative mutant 05A02 exhibited reduced binding to collagen and laminin but retained that to fibronectin. This gene was detected in some strains of S. mutans. Therefore, the cnm gene encoded a new strain-specific member of the collagen-binding adhesin family.

Crystal structure of hemoglobin from mouse (Mus musculus) compared with those from other small animals and humans

2021 ◽  
Vol 77 (4) ◽  
pp. 113-120
Author(s):  
Selvarajan Sigamani Sundaresan ◽  
Pandian Ramesh ◽  
Nagaraj Shobana ◽  
Thangaraj Vinuchakkaravarthy ◽  
Sayed Yasien ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Mus Musculus ◽  
Structural Features ◽  
Small Animals ◽  
Orthorhombic Space Group ◽  
Primary Amino ◽  
The Difference ◽  
Function Relationship

Mice (Mus musculus) are nocturnal small animals belonging to the rodent family that live in burrows, an environment in which significantly high CO2 levels prevail. It is expected that mouse hemoglobin (Hb) plays an important role in their adaptation to living in such a high-CO2 environment, while many other species cannot. In the present study, mouse Hb was purified and crystallized at a physiological pH of 7 in the orthorhombic space group P212121; the crystals diffracted to 2.8 Å resolution. The primary amino-acid sequence and crystal structure of mouse Hb were compared with those of mammalian Hbs in order to investigate the structure–function relationship of mouse Hb. Differences were observed from guinea pig Hb in terms of amino-acid sequence and from cat Hb in overall structure (in terms of r.m.s.d.). The difference in r.m.s.d. from cat Hb may be due to the existence of the molecule in a conformation other than the R-state. Analysis of tertiary- and quaternary-structural features, the α1β2 interface region and the heme environment without any ligands in all four heme groups showed that mouse methemoglobin is in an intermediate state between the R-state and the T-state that is much closer to the R-state conformation.

scholarly journals Identification of cytokine-induced neutrophil chemoattractants (CINC), rat GRO/CINC-2α and CINC-2 β, produced by granulation tissue in culture: purification, complete amino acid sequences and characterization

1994 ◽  
Vol 301 (2) ◽  
pp. 545-550 ◽  
Author(s):  
H Nakagawa ◽  
N Komorita ◽  
F Shibata ◽  
A Ikesue ◽  
K Konishi ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Granulation Tissue ◽  
Pcr Amplification ◽  
Neutrophil Infiltration ◽  
Amino Acid Sequences ◽  
Terminal Amino Acid ◽  
Reverse Transcription Pcr ◽  
Terminal Amino ◽  
The Difference

Four basic neutrophil chemotactic factors (chemokines) have been purified from conditioned medium of granulation tissue obtained from carrageenin-induced inflammation in the rat. On the basis of their N-terminal amino acid sequences, one of the chemokines was identical with rat GRO/cytokine-induced neutrophil chemoattractant (CINC) which we reported previously, and another was identical with rat macrophage inflammatory protein-2 (MIP-2). Two other chemokines were novel chemoattractants related to MIP-2. The novel chemokines are referred to as rat GRO/CINC-2 alpha and CINC-2 beta, and consequently CINC and rat MIP-2 are renamed rat GRO/CINC-1 and CINC-3 respectively. The complete amino acid sequences of purified CINC-2 alpha and CINC-3 were determined by analysis of the fragments isolated from proteinase V8-treated CINCs. The cDNA for CINC-2 beta was cloned by reverse transcription/PCR amplification using specific primers starting with total RNA extracted from lipopolysaccharide-stimulated rat macrophages. A comparison of the amino acid sequence encoded by the cDNA with the N-terminal amino acid sequence of purified CINC-2 beta revealed that mature CINC-2 beta is a 68-residue chemoattractant produced by cleavage of a 32-residue signal peptide. The difference in amino acid sequences between CINC-2 alpha and CINC-2 beta consisted of only three C-terminal residues. Rat GRO/CINC-2 alpha is a major chemokine, and the four purified chemokines have similar chemotactic activity, suggesting that they contribute to neutrophil infiltration into inflammatory sites in rats.

The ADP-ribosylating thermozyme from Sulfolobus solfataricus is a DING protein

2009 ◽  
Vol 390 (1) ◽  
Author(s):  
Antimo Di Maro ◽  
Anna De Maio ◽  
Sabrina Castellano ◽  
Augusto Parente ◽  
Benedetta Farina ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Sulfolobus Solfataricus ◽  
Terminal Region ◽  
High Similarity ◽  
Partial Amino Acid Sequence ◽  
Tryptic Peptides ◽  
Ding Protein ◽  
N Terminus

Abstract The partial amino acid sequence of the sulfolobal thermoprotein biochemically characterized as poly(ADP-ribose)polymerase-like enzyme overlaps those of DING proteins. This group of proteins, widely occurring in animals, plants and eubacteria, shows a characteristic and highly conserved N-terminus, DINGGGATL. The sequence of the N-terminal region and of the analyzed tryptic peptides of the sulfolobal thermozyme shows a high similarity with most of the DING proteins from databases. This is the first example of a DING protein from a sulfolobal source.

scholarly journals Different Rifampin Sensitivities of Escherichia coli and Mycobacterium tuberculosis RNA Polymerases Are Not Explained by the Difference in the β-Subunit Rifampin Regions I and II

2005 ◽  
Vol 49 (4) ◽  
pp. 1587-1590 ◽  
Author(s):  
N. Zenkin ◽  
A. Kulbachinskiy ◽  
I. Bass ◽  
V. Nikiforov
Keyword(s):  
Escherichia Coli ◽  
Amino Acids ◽  
Mycobacterium Tuberculosis ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Rna Polymerase ◽  
Β Subunit ◽  
E Coli ◽  
Increased Sensitivity ◽  
The Difference

ABSTRACT Mycobacterium tuberculosis RNA polymerase is 1,000-fold more sensitive to rifampin than Escherichia coli RNA polymerase. Chimeric E. coli RNA polymerase in which the β-subunit segment encompassing rifampin regions I and II (amino acids [aa] 463 through 590) was replaced with the corresponding region from M. tuberculosis (aa 382 through 509) did not show an increased sensitivity to the antibiotic. Thus, the difference in amino acid sequence between the rifampin regions I and II of the two species does not account for the difference in rifampin sensitivity of the two polymerases.

Characterization of two forms of cationic peroxidase from cultured peanut cells

1992 ◽  
Vol 70 (2) ◽  
pp. 166-169 ◽  
Author(s):  
James P. O'Donnell ◽  
Lianglu Wan ◽  
R. B. van Huystee
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Molecular Mass ◽  
Concanavalin A ◽  
Specific Activity ◽  
Calcium Content ◽  
Molecular Forms ◽  
The Difference ◽  
Peanut Peroxidase

Two forms of cationic peroxidase from peanut cells were differentiated by concanavalin A affinity chromatography. They differed in molecular mass as well as concanavalin A binding, leading to the initial suggestion that they represented two isozymes of peroxidase. However, similar values for the specific activity, Soret absorption, calcium content, and peptide molecular mass were observed for each of the forms. Therefore, the binding and nonbinding fractions most likely represent two molecular forms of cationic peanut peroxidase, rather than two distinct cationic isozymes. The difference between these two forms is discussed in terms of glycosylation. Through the amino acid sequence analysis of the formic acid treated peptide, the cationic isozyme has been shown to be identical in amino acid sequence to the cDNA clone PNC1.Key words: peanut, peroxidase, glycan, characterization, sequence.

scholarly journals Dissecting the Interaction Deficiency of a Cartilaginous Fish Digestive Lipase with Pancreatic Colipase: Biochemical and Structural Insights

2020 ◽  
Vol 2020 ◽  
pp. 1-10
Author(s):  
Neila Achouri ◽  
Màrius Tomàs-Gamisans ◽  
Soumaya Triki ◽  
Francisco Valero ◽  
Nabil Miled ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Bile Salts ◽  
Structural Model ◽  
Catalytic Triad ◽  
Cartilaginous Fish ◽  
Residue Level ◽  
High Similarity ◽  
Structural Insights

A full-length cDNA encoding digestive lipase (SmDL) was cloned from the pancreas of the smooth-hound (Mustelus mustelus). The obtained cDNA was 1350 bp long encoding 451 amino acids. The deduced amino acid sequence has high similarity with known pancreatic lipases. Catalytic triad and disulphide bond positions are also conserved. According to the established phylogeny, the SmDL was grouped with those of tuna and Sparidae lipases into one fish digestive lipase cluster. The recently purified enzyme shows no dependence for bile salts and colipase. For this, the residue-level interactions between lipase-colipase are yet to be clearly understood. The structural model of the SmDL was built, and several dissimilarities were noticed when analyzing the SmDL amino acids corresponding to those involved in HPL binding to colipase. Interestingly, the C-terminal domain of SmDL which holds the colipase shows a significant role for colipase interaction. This is apt to prevent the interaction between fish lipase and the pancreatic colipase which and can provide more explanation on the fact that the classical colipase is unable to activate the SmDL.

The staining pattern of the tropomyosin sequence is displayed in a new paracrystal

1986 ◽  
Vol 44 ◽  
pp. 150-151
Author(s):  
M.K. Lamvik ◽  
L.L. Klatt
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Staining Pattern ◽  
Banding Patterns ◽  
Mass Thickness ◽  
New Form

Tropomyosin paracrystals have been used extensively as test specimens and magnification standards due to their clear periodic banding patterns. The paracrystal type discovered by Ohtsuki1 has been of particular interest as a test of unstained specimens because of alternating bands that differ by 50% in mass thickness. While producing specimens of this type, we came across a new paracrystal form. Since this new form displays aligned tropomyosin molecules without the overlaps that are characteristic of the Ohtsuki-type paracrystal, it presents a staining pattern that corresponds to the amino acid sequence of the molecule.

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